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2.5 years ago
Roy
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10
Hello all,
I use CNVkit for my workflow with the WES bam files. I am curious that this kit had a function to calculate loss of heterozygosity (loh) via a vcf file on an old version of this. I am actually interested in analyzing for LOH, so is there an alternative? I see a tumor heterogeneity section I could follow on CNVkit, but not sure what to do. Any advice is appreciated; maybe I can write my own LOH calculation via my VCFs?
Thanks, Roy
I regularly use FACETS for this purpose. You can find the paper here if you are interested.
Thanks, this looks intriguing. I only have the tumor BAM file, is the normal required?